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Mech Dev March 1, 2005; 122 (3): 365-439.

An atlas of differential gene expression during early Xenopus embryogenesis.

Pollet N , Muncke N , Verbeek B , Li Y , Fenger U , Delius H , Niehrs C .

We have carried out a large-scale, semi-automated whole-mount in situ hybridization screen of 8369 cDNA clones in Xenopus laevis embryos. We confirm that differential gene expression is prevalent during embryogenesis since 24% of the clones are expressed non-ubiquitously and 8% are organ or cell type specific marker genes. Sequence analysis and clustering yielded 723 unique genes displaying a differential expression pattern. Of these, 18% were already described in Xenopus, 47% have homologs and 35% are lacking significant sequence similarity in databases. Many of them encode known developmental regulators. We classified 363 of the 723 genes for which a Gene Ontology annotation for molecular function could be attributed and found ''DNA binding'' and ''enzyme'' the most represented terms. The most common protein domains encoded in these embryonic, differentially expressed genes are the homeobox and RNA Recognition Motif (RRM). Fifty-nine putative orthologs of human disease genes, and 254 organ or cell specific marker genes were identified. Markers were found for nasal placode and archenteron roof, organs for which a specific marker was previously unavailable. Markers were also found for novel subdomains of various other organs. The tissues for which most markers were found are muscle and epidermis. Expression of cell cycle regulators fell in two classes, containing proliferation-promoting and anti-proliferative genes, respectively. We identified 66 new members of the BMP4, chromatin, endoplasmic reticulum, and karyopherin synexpression groups, thus providing a first glimpse of their probable cellular roles. Cluster analysis of tissues to measure tissue relatedness yielded some unorthodox affinities besides expectable lineage relationships. In conclusion, this study represents an atlas of gene expression patterns, which reveals embryonic regionalization, provides novel marker genes, and makes predictions about the functional role of unknown genes.

PubMed ID: 15763213
Article link: Mech Dev

Genes referenced: epn3 gjb2 has1 nt5c2 ahnak sgk1 tent2 has-rs sox17a spam1 bin1 rreb1 mylpf atp2a1 srl myh4 thbs4 myod1 c19orf47 myh8 carns1 hspb1 rab5b wbp11 ppp1r3c.1 synm c12orf4 fndc3a ppif samd4b apob loc108715171 prkd1 rbfox2 rbm24 fxr1 dlst lgals3 aldh16a1 acsl1 gstp1 rhoc elovl7 tubb4b itm2a glud1 gsto1 abr tuba1cl.3 tepp bmp4 fen1 gnao1 mespa ppib tbl1x

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